The light harvesting antenna in eukaryotic algae is a complex component of the multi-subunit photosystem complexes. In response to environment conditions, such as variable irradiance, the composition can be appropriately modified as part of an acclimation response. Components of this variable component of the photosystem include multiple light harvesting polypeptides and pigments, such as chlorophyll and a variety of carotenoids. The light harvesting antenna in Nannochloropsis includes auxiliary pigments including vaucheriaxanthin and violaxanthin. Three violaxanthin-chlorophyll a binding protein (VCP) genes have been identified in the Nannochloropsis genome. While the precise function of these proteins and mechanism of their interaction with other components of the photosystem super-complexes are only poorly characterized, they are members of the LHC family that are believed to function in the binding of auxiliary light harvesting antenna components, including violaxanthin, vaucheriaxanthin, and chlorophyll. In vascular plants and green algae, light-harvesting complexes (LHC) are composed of a family of intrinsic membrane polypeptides that non-covalently bind chlorophyll (chl) a, chl b, xanthophylls, and carotenoids; these polypeptides have been designated LHC (Green and Durnford, 1996 Annu. Rev. Plant Physiol. Plant Mol. Biol. 47:685-714; Grossman et al., 1995, Ann. Rev. Genetics 29:231-88). The LHC polypeptides are encoded by a nuclear gene family that has been extensively examined in vascular plants (Bhaya and Grossman, 1993, Nucleic Acids Res. 21:4458-66; Green and Durnford, 1996, Annu. Rev. Plant Physiol. Plant Mol. Biol. 47:685-714). Polypeptides related to plant and green algae LHCs are present in the chromophytic algae (algae that have chlorophyll c), such as the diatoms (bacillariophytes), chrysophytes, and dinoflagellates. The major LHC of the chromophytes is a fucoxanthin-chl a/c complex (FCPC), that harvests light energy and transfers the absorbed energy to chl a of the photosynthetic reaction centers (Joshi-Deo et al., 2010, J. Exp. Bot., June 61(11):3079-87). The constituent polypeptides of this complex, designated fucoxanthin-chlorophyll binding proteins (FCPs) are usually between 17 kDa and 22 kDa and share significant similarity to the LHC of vascular plants (Fawley and Grossman, 1986, Plant Physiol. May; 81(1):149-55; Caron and Brown, 1987, Plant Cell Physiol. 28:775-785; Green et al, 1991, Trends Biochem. Sci. 16:181-6). Sequences of the FCPs have been deduced from gene sequences characterized from diatoms, phaeophytes, a raphidophyte, a chrysophyte, and a haptophyte (Bhaya and Grossman, 1993, Nucleic Acids Res. 21:4458-66). Amino acid sequence comparisons between FCP and LHC polypeptides reveal extensive sequence similarities, especially in the three chl-binding domains that span the thylakoid membranes. The greatest similarities between the FCPs and the LHCs are within or near the first and third membrane-spanning domains; similarities include conserved residues that are involved in chl binding and are critical for the maintenance of the proper tertiary structure of the protein (Grossman et al., 1990, Mol. Gen. Genet. 224:91-100; Kuhlbrandt et al., 1994, Nature 367:614-21; Sukenik et al, 2000, J. Phycol. 36, 563-570). In the diatoms and brown algae, the FCPs are encoded in the nuclear genome by a family of 6 to 12 conserved genes (Bhaya and Grossman, 1993, Nucleic Acids Res. 21:4458-66; Apt et al., 1995, Mol. Gen. Genet. 246:455-64; Durnford et al., 1996, Mol. Gen. Genet. 253: 377-86; Eppard and Rhiel, 1998, Mol. Gen. Genet. 260:335-45). The eustigmatophyte algae, along with the diatoms, phaeophytes, xanthophytes, raphidophytes, and chrysophytes, belong to the heterokont class of algae (Ochrophytes). In contrast to vascular plants and most other algal groups, eustigmatophyte algae have neither chl b nor chl c. The major polypeptide of their LHC is a violaxanthin-chl a binding protein (VCP). Initial characterization of a LHC from Nannochloropsis was reported by Brown (1987, Plant Physiol. 66:434-7) and from other eustigmatophyte species by Arsalane et al. (1992 J. Phycol. 28:32-6). The VCPs, which bind violaxanthin and chlorophyll a, are structurally similar to FCPs (Sukenik et al., 1992, Plant and Cell Physiol. 33:1041-48; Sukenik et al, 2000).